ScopeViewer: A Browser-Based Solution for Visualizing Spatial Transcriptomics Data

Abstract

MotivationSpatial transcriptomics (ST) enables a high-resolution interrogation of molecular characteristics within specific spatial contexts and tissue morphology. Despite its potential, visualization of ST data is a challenging task due to the complexities in handling, sharing and visualizing large image datasets together with molecular information. ResultsWe introduce ScopeViewer, a browser-based software designed to overcome these challenges. ScopeViewer offers the following functionalities: (1) It visualizes large image data and associated annotations at various zoom levels, allowing for intricate exploration of the data; (2) It enables dual interactive viewing of the original images along with their annotations, providing a comprehensive understanding of the context; (3) It displays spatial molecular features with optimized bandwidth, ensuring a smooth user experience; and (4) It bolsters data security by circumventing data transfers. AvailabilityScopeViewer is available at: https://datacommons.swmed.edu/scopeviewer ContactXiaowei.Zhan@UTSouthwestern.edu, Guanghua.Xiao@UTSouthwestern.edu Supplementary informationSupplementary data are available at Bioinformatics online.